Fig. 7
During Shaker, conformational changes of the pentapeptide KQTSV are observed, while remains bound to its pocket on the PDZ domain (System 10). Red sticks represent the native ligand conformation from PDB (1be9). Teal sticks represent ligand conformations at different Shaker stages starting with the conformation right after Wrapper (1), and continuing with conformation after MDBSA (2), and after MDF (3). The changes of target-ligand interaction energy (ELJ) and the RMSD during the MD stages in the Shaker protocol are plotted below the structural snapshots. See also Additional file 3: Supporting Movie 2 for further details of conformational changes